I am having problem installing affy package from source on my Debian system with R-2.8.0. The earlier version (from bioc2.2) works fine with R-2.7.0 on the same system. Any idea of what is going wrong with the new version? ################################################################### > sessionInfo() R version 2.8.0 (2008-10-20) i686-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.0 ################################################################## > source("http://bioconductor.org/biocLite.R") > biocLite("affy") ............................. * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" -fpic -g -O2 -c chipbackground.c -o chipbackground.o gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" -fpic -g -O2 -c getall_locations.c -o getall_locations.o gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" -fpic -g -O2 -c mas5calls.c -o mas5calls.o gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" -fpic -g -O2 -c rma2.c -o rma2.o rma2.c:108:29: error: rma_background4.h: No such file or directory rma2.c:119:45: error: preprocessCore_background_stubs.c: No such file or directory rma2.c:123:31: error: R_subColSummarize.h: No such file or directory rma2.c:124:37: error: R_subColSummarize_stubs.c: No such file or directory rma2.c: In function 'do_RMA2': rma2.c:133: warning: implicit declaration of function 'R_subColSummarize_medianpolish_log' rma2.c:133: warning: assignment makes pointer from integer without a cast rma2.c: In function 'rma_c_complete': rma2.c:248: warning: implicit declaration of function 'rma_bg_correct' make: *** [rma2.o] Error 1 chmod: cannot access `/usr/local/lib/R/site-library/affy/libs/*': No such file or directory ERROR: compilation failed for package 'affy' ** Removing '/usr/local/lib/R/site-library/affy' ** Restoring previous '/usr/local/lib/R/site-library/affy' The downloaded packages are in /tmp/RtmprdJr3r/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'affy' had non-zero exit status -- Mizanur Khondoker Division of Pathway Medicine (DPM) The University of Edinburgh Medical School The Chancellor's Building 49 Little France Crescent Edinburgh EH16 4SB United Kingdom Tel: +44 (0) 131 242 6287 Fax: +44 (0) 131 242 6244 http://www.pathwaymedicine.ed.ac.uk/ [[alternative HTML version deleted]]

"Mizanur Khondoker" <mizanur.khondoker at="" ed.ac.uk=""> writes: > I am having problem installing affy package from source on my Debian system > with R-2.8.0. The earlier version (from bioc2.2) works fine with R-2.7.0 on > the same system. > Any idea of what is going wrong with the new version? I think you're installing over an existing installation, and you have an outdated version of the 'preprocessCore' package that needs to be updated. In a NEW R session, follow the 'Update installed Bioconductor packages' directions at http://bioconductor.org/docs/install/ No need to cross-post. Martin > > ################################################################### >> sessionInfo() > R version 2.8.0 (2008-10-20) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.8.0 > > ################################################################## >> source("http://bioconductor.org/biocLite.R") >> biocLite("affy") > > ............................. > > * Installing *source* package 'affy' ... > creating cache ./config.cache > checking how to run the C preprocessor... cc -E > checking for main in -lz... yes > checking for zlib.h... yes > checking if zlib version >= 1.1.3... yes > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 > -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" > -fpic -g -O2 -c chipbackground.c -o chipbackground.o > gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 > -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" > -fpic -g -O2 -c getall_locations.c -o getall_locations.o > gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 > -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" > -fpic -g -O2 -c mas5calls.c -o mas5calls.o > gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1 > -I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include" > -fpic -g -O2 -c rma2.c -o rma2.o > rma2.c:108:29: error: rma_background4.h: No such file or directory > rma2.c:119:45: error: preprocessCore_background_stubs.c: No such file or > directory > rma2.c:123:31: error: R_subColSummarize.h: No such file or directory > rma2.c:124:37: error: R_subColSummarize_stubs.c: No such file or directory > rma2.c: In function 'do_RMA2': > rma2.c:133: warning: implicit declaration of function > 'R_subColSummarize_medianpolish_log' > rma2.c:133: warning: assignment makes pointer from integer without a cast > rma2.c: In function 'rma_c_complete': > rma2.c:248: warning: implicit declaration of function 'rma_bg_correct' > make: *** [rma2.o] Error 1 > chmod: cannot access `/usr/local/lib/R/site-library/affy/libs/*': No such > file or directory > ERROR: compilation failed for package 'affy' > ** Removing '/usr/local/lib/R/site-library/affy' > ** Restoring previous '/usr/local/lib/R/site-library/affy' > > The downloaded packages are in > /tmp/RtmprdJr3r/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'affy' had non-zero exit status > > > > > -- > Mizanur Khondoker > Division of Pathway Medicine (DPM) > The University of Edinburgh Medical School > The Chancellor's Building > 49 Little France Crescent > Edinburgh EH16 4SB > United Kingdom > > Tel: +44 (0) 131 242 6287 > Fax: +44 (0) 131 242 6244 > http://www.pathwaymedicine.ed.ac.uk/ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793